How are you starting the workflows associated to each list item? Are you able to use the workflow status column to check to see if it is "In Progress" or some other value that would you to tell that the workflow was currently in progress - I would probably do something along these lines and it could vary slightly depending on your launch mechanism.

The Workflow Status field is automatically generated by Nintex. It is a text field. Normally when you create a workflow, it automatically gets displayed in the list view. However, you can decide to not display it.

Again, if it is a scheduled workflow you can use the 'Set Workflow Status' to change items to the status you want it to be. But when it is not scheduled this will happen automatically.